Background The growth rate is central for the development of cells in all organisms. However, little is known about the impact of changing growth rates. We have used continuous cultures to control the growth rate and study the transcriptional programme of the model eukaryote Saccharomyces cerevisiae with generation times varying between 2 and 35 hours. Results A total of 5,930 transcripts were identified at the different growth rates studied. Consensus clustering of these revealed that half of all yeast genes are affected by the specific growth rate, and that the changes are similar to those found when cells are exposed to different types of stress (more than 80% overlap). Genes with decreased transcript levels in response to faster growth are largely of unknown function (more than 50%) while genes with increased transcript levels are involved in macromolecular biosynthesis such as those encoding ribosomal proteins. This group also covers most targets of the transcriptional activator, RAP1, which is also known to be involved in replication. A positive correlation between the location of replication origins and the location of growth-regulated genes, suggests a role for replication in growth rate regulation. Conclusions Our data show that the cellular growth rate has paramount influence on transcriptional regulation. This, in turn, implies that one should be cautious when comparing mutants with different growth rates. The results also indicate that much of the regulation is coordinated via the chromosomal location of the affected genes, which may be valuable information for the control of heterologous gene expression in metabolic engineering.